#!/usr/bin/perl -w
#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
#
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License.
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#
=head1 NMPDR Status Checker
This script examines all of the genomes and displays the NMPDR group for each.
The currently-supported command-line options are as follows.
=over 4
=item user
Name suffix to be used for log files. If omitted, the PID is used.
=item trace
Numeric trace level. A higher trace level causes more messages to appear. The
default trace level is 2. Tracing will be directly to the standard output
as well as to a CIC file in the FIG temporary directory,
where I is the value of the B option above.
=item sql
If specified, turns on tracing of SQL activity.
=item background
Save the standard and error output to files. The files will be created
in the FIG temporary directory and will be named CIC and
CIC, respectively, where I is the value of the
B option above.
=item h
Display this command's parameters and options.
=item phone
Phone number to message when the script is complete.
=back
=cut
use strict;
use Tracer;
use FIG;
use Cwd;
use File::Copy;
use File::Path;
# Get the command-line options and parameters.
my ($options, @parameters) = StandardSetup([qw(FIG) ],
{
phone => ["", "phone number (international format) to call when load finishes"],
},
"",
@ARGV);
# Set a variable to contain return type information.
my $rtype;
# Insure we catch errors.
eval {
# Get the FIG object.
my $fig = FIG->new();
# Get a list of all the genomes.
my $genomes = $fig->genome_list();
Trace(scalar(@{$genomes}) . " found.") if T(3);
# Loop through the list.
for my $genome (@{$genomes}) {
# Get the genome ID and name.
my ($genomeID, $genomeName) = @{$genome};
# Only proceed if the genome is complete. Otherwise, it's not part of NMPDR.
my $flag = $fig->is_complete($genomeID);
Trace("Complete flag for $genomeID is $flag.") if T(4);
if ($flag) {
# Compute the NMPDR group.
my $nmpdrFile = "$FIG_Config::organisms/$genomeID/NMPDR";
if (-e $nmpdrFile) {
# Get the NMPDR group from the file contents.
my ($nmpdrGroup) = Tracer::GetFile($nmpdrFile);
# Trace the result.
Trace("$genomeID ($genomeName) = $nmpdrGroup") if T(2);
}
} else {
# Denote this is not an NMPDR genome.
Trace("$genomeID ($genomeName) not used.") if T(3);
}
}
Trace("Processing complete.") if T(2);
};
if ($@) {
Trace("Script failed with error: $@") if T(0);
$rtype = "error";
} else {
Trace("Script complete.") if T(2);
$rtype = "no error";
}
if ($options->{phone}) {
my $msgID = Tracer::SendSMS($options->{phone}, "NMPDR Status Checker terminated with $rtype.");
if ($msgID) {
Trace("Phone message sent with ID $msgID.") if T(2);
} else {
Trace("Phone message not sent.") if T(2);
}
}
1;